Commits · aa8634519eb4a82ab3f10dee9497c13b40a0e86d · Mirrors / mutalyzer

Apr 07, 2011

Updated README and INSTALL files. · aa863451

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@259 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

aa863451

Updated installation instructions. · 95d76894

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@258 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

95d76894

Fixed installation scripts. · 25f0d9c1

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@257 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

25f0d9c1

Revised installation instructions. Added pre-install script. · ddffc86a

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@256 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ddffc86a

Fixed batch daemon init script. · 20196ccb

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@255 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

20196ccb

Use environment variable MUTALYZER_ENV=test to use testing settings. · d2c3743f

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@254 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

d2c3743f

Completed post-install script. Related fixes. · 9289bd3f

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@253 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

9289bd3f

Apr 06, 2011

Some reorganisation. Added post-install script. · 6c4f4bdd

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@252 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6c4f4bdd

Apr 05, 2011

Merging r249 from trunk. · 65b9196f

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@251 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

65b9196f

Sort of working version with setuptools. · b70090c6

Vermaat authored 14 years ago

Locations and python paths are correct with respect to the setup.py file.
For development, use
  svn up && python setup.py develop
and for deployment use
  svn up && sudo python setup.py install



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@250 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b70090c6

Added a line about logging in the disclaimer. · 83431124

Laros authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@249 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

83431124

Further changes to setup.py. · 0c3e89d1

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@248 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0c3e89d1

Moved templates/ to mutalyzer/templates/. · 835de4de

Vermaat authored 14 years ago

This is debatable, but makes distribution much easier. Setuptools no longer
ignores the templates this way and stores them along the mutalyzer package,
so they will be globally available.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@247 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

835de4de

Renamed ./examples to ./extras. · bccd091a

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@246 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

bccd091a

Apr 04, 2011

Added setuptools setup.py file. · a4bf5e55

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@245 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a4bf5e55

- Moved tests from ./mutalyzer/tests/ to ./tests/. · e2b51a1f

Vermaat authored 14 years ago

- Added error recovery to batch daemon.
- Added example init script for batch daemon.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@244 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e2b51a1f

The bin/find_log_bugs script is now executable. · 98a55a55

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@243 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

98a55a55

Merged 236 from trunk. · 352e2026

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@242 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

352e2026

Merge 235 from trunk. · 85b1a786

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@241 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

85b1a786

Added SOAP example clients. · 2595121b

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@240 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

2595121b

Apr 01, 2011

Added detection for running batch daemon. · 528bd312

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@239 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

528bd312

Rewrote the batch job processing daemon. · c31da7f7

Vermaat authored 14 years ago

It now shuts down gracefully, completing the current job item. General
daemon handling code is now also better, including PID file handling.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@238 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c31da7f7

Fix: don't process the other raw variants after an error occured. · b249fac0

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@237 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b249fac0

Mar 31, 2011

Added a small script that detects started but unfinished jobs by inspecting the · 6b169b49
Laros authored 14 years ago
```
log file.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@236 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
6b169b49

Fixed a bug that was triggered when a translation of non-dna is attempted. This · 30b16f81

Laros authored 14 years ago

can happen when the reference sequence contains IUPAC codes.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@235 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

30b16f81

Keep track of removed splice sites in Mutator instance. · df44318b

Vermaat authored 14 years ago

This implements the revert mentioned in the previous commit and now this
branch fully merged the first part of exon-deletions-branch. The second
part of that branch is about unknown offsets, but that implementation is
not yet fit to be merged.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@234 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

df44318b

Deletions of entire exons (even number of consecutive splice sites). · e13db7df

Vermaat authored 14 years ago

This merges the first part of exon-deletions-branch (the second part concerns
unknown exon offsets, denoted with the ? character). Except that we now keep
track of removed splice sites in the transcript, instead of in the Mutator
instance. I guess the latter was better, so we will probably revert to storing
this in the Mutator instance.

Issue #35.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@233 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e13db7df

Some updates to the batch job runner. It is now an executable in bin/. · 4b9d36e6

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@232 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4b9d36e6

Fixed the batch job runner. · 58386913

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@231 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

58386913

Log more detailed info in case of dbSNP errors. · f6b21018

Vermaat authored 14 years ago


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@230 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f6b21018

Fixed webservice to use correct package path. · 954ecc01

Vermaat authored 14 years ago


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@229 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

954ecc01

Fixed some formatting errors in name checker web interface. · 840559e0

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@228 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

840559e0

Mar 30, 2011

Updated web interface output for the name checker. · 7294a4c8

Vermaat authored 14 years ago

Static transcript information should now also be shown if there were errors
with the variant.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@227 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7294a4c8

Mar 29, 2011

Nothing much. · c5fa349a

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@226 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c5fa349a

Unit tests should not be executable. · a1c2b8eb

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@225 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a1c2b8eb

Updated unit tests. Now using the nose Python testing framework. · 3f15b518

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@224 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

3f15b518

Finished first refactoring of the variant checker code. · 2d73e50f

Vermaat authored 14 years ago

Mostly this was adding documentation, cleaning code, and adding exception
paths.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@223 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

2d73e50f

Mar 28, 2011

Refactoring configuration and file paths. · 6150d6dd

Vermaat authored 14 years ago

- Ditched use of web.session, just use web.cookies.
- Added detection of configuration file location.
- Removed ./var directory, everything is now in standard locations, but also
  configurable.
- Added more standard version management.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@222 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6150d6dd

Some file shuffling refactoring. · 6c3db044

Vermaat authored 14 years ago

- Moved mail.txt to templates/batch-mail.txt.
- Moved Obsoleted.txt and TODO into a README.
- Move mutalyzer.sql into INSTALL.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@221 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6c3db044

Mar 25, 2011

Updates in name checker error messages. · 10fa9ef8

Vermaat authored 14 years ago


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@220 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

10fa9ef8